Merge pull request openalea#46 from AurelienBesnier/master

updating numpy + vtk functions

.gitignore

@@ -106,4 +106,7 @@ venv.bak/
 /site
 
 # mypy
-.mypy_cache/
+.mypy_cache/
+
+# vscode
+.vscode

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: openalea.phenomenal
-  version: "1.9.2"
+  version: "1.9.3"
 
 source:
   path: ..
@@ -10,12 +10,12 @@ build:
   preserve_egg_dir: True
   string: phenomenal
   script: 
-    - {{PYTHON}} setup.py build_ext -j{{ CPU_COUNT }}
     - {{ PYTHON }} -m pip install . -vv
 
 requirements:
   host:
     - python
+    - setuptools
     - numpy 
     - scipy
     - cython

src/openalea/phenomenal/calibration/transformations.py

@@ -338,7 +338,7 @@ def rotation_matrix(angle, direction, point=None):
     M[:3, :3] = R
     if point is not None:
         # rotation not around origin
-        point = numpy.array(point[:3], dtype=numpy.float64, copy=False)
+        point = numpy.array(point[:3], dtype=numpy.float64)
         M[:3, 3] = point - numpy.dot(R, point)
     return M
 
@@ -356,7 +356,7 @@ def rotation_from_matrix(matrix):
     True
 
     """
-    R = numpy.array(matrix, dtype=numpy.float64, copy=False)
+    R = numpy.array(matrix, dtype=numpy.float64)
     R33 = R[:3, :3]
     # direction: unit eigenvector of R33 corresponding to eigenvalue of 1
     w, W = numpy.linalg.eig(R33.T)
@@ -491,12 +491,11 @@ def projection_matrix(point, normal, direction=None,
 
     """
     M = numpy.identity(4)
-    point = numpy.array(point[:3], dtype=numpy.float64, copy=False)
+    point = numpy.array(point[:3], dtype=numpy.float64)
     normal = unit_vector(normal[:3])
     if perspective is not None:
         # perspective projection
-        perspective = numpy.array(perspective[:3], dtype=numpy.float64,
-                                  copy=False)
+        perspective = numpy.array(perspective[:3], dtype=numpy.float64)
         M[0, 0] = M[1, 1] = M[2, 2] = numpy.dot(perspective-point, normal)
         M[:3, :3] -= numpy.outer(perspective, normal)
         if pseudo:
@@ -509,7 +508,7 @@ def projection_matrix(point, normal, direction=None,
         M[3, 3] = numpy.dot(perspective, normal)
     elif direction is not None:
         # parallel projection
-        direction = numpy.array(direction[:3], dtype=numpy.float64, copy=False)
+        direction = numpy.array(direction[:3], dtype=numpy.float64)
         scale = numpy.dot(direction, normal)
         M[:3, :3] -= numpy.outer(direction, normal) / scale
         M[:3, 3] = direction * (numpy.dot(point, normal) / scale)
@@ -552,7 +551,7 @@ def projection_from_matrix(matrix, pseudo=False):
     True
 
     """
-    M = numpy.array(matrix, dtype=numpy.float64, copy=False)
+    M = numpy.array(matrix, dtype=numpy.float64)
     M33 = M[:3, :3]
     w, V = numpy.linalg.eig(M)
     i = numpy.where(abs(numpy.real(w) - 1.0) < 1e-8)[0]

src/openalea/phenomenal/mesh/algorithms.py

@@ -10,7 +10,7 @@
 from __future__ import division, print_function, absolute_import
 
 import vtk
-import vtk.util.numpy_support
+import vtkmodules.util.numpy_support
 import numpy
 import math
 import skimage.measure

src/openalea/phenomenal/mesh/formats.py

@@ -10,7 +10,8 @@
 from __future__ import division, print_function, absolute_import
 
 import vtk
-import vtk.util.numpy_support
+import vtkmodules.util.numpy_support
+import vtkmodules
 
 from .vtk_transformation import (from_vertices_faces_to_vtk_poly_data)
 # ==============================================================================
@@ -47,17 +48,17 @@ def read_ply_to_vertices_faces(filename):
 
     vtk_poly_data = ply_reader.GetOutput()
 
-    vertices = vtk.util.numpy_support.vtk_to_numpy(
+    vertices = vtkmodules.util.numpy_support.vtk_to_numpy(
         vtk_poly_data.GetPoints().GetData())
 
-    faces = vtk.util.numpy_support.vtk_to_numpy(
+    faces = vtkmodules.util.numpy_support.vtk_to_numpy(
         vtk_poly_data.GetPolys().GetData())
 
     faces = faces.reshape((len(faces) // 4, 4))
 
     colors = vtk_poly_data.GetPointData().GetScalars()
     if colors is not None:
-        colors = vtk.util.numpy_support.vtk_to_numpy(colors)
+        colors = vtkmodules.util.numpy_support.vtk_to_numpy(colors)
 
     return vertices, faces[:, 1:], colors
 

src/openalea/phenomenal/mesh/vtk_transformation.py

@@ -10,7 +10,7 @@
 from __future__ import division, print_function, absolute_import
 
 import vtk
-import vtk.util.numpy_support
+import vtkmodules.util.numpy_support
 import operator
 
 # ==============================================================================
@@ -105,10 +105,10 @@ def make_vtk_id_list(it):
 
 def from_vtk_poly_data_to_vertices_faces(vtk_poly_data):
 
-    vertices = vtk.util.numpy_support.vtk_to_numpy(
+    vertices = vtkmodules.util.numpy_support.vtk_to_numpy(
         vtk_poly_data.GetPoints().GetData())
 
-    faces = vtk.util.numpy_support.vtk_to_numpy(
+    faces = vtkmodules.util.numpy_support.vtk_to_numpy(
         vtk_poly_data.GetPolys().GetData())
 
     faces = faces.reshape((len(faces) // 4, 4))
@@ -126,12 +126,12 @@ def from_numpy_matrix_to_vtk_image_data(data_matrix):
     image_data.SetSpacing(1.0, 1.0, 1.0)
 
     if vtk.VTK_MAJOR_VERSION < 6:
-        image_data.SetScalarType(vtk.util.numpy_support.get_vtk_array_type(
+        image_data.SetScalarType(vtkmodules.util.numpy_support.get_vtk_array_type(
             data_matrix.dtype))
         image_data.SetNumberOfScalarComponents(1)
         image_data.AllocateScalars()
     else:
-        image_data.AllocateScalars(vtk.util.numpy_support.get_vtk_array_type(
+        image_data.AllocateScalars(vtkmodules.util.numpy_support.get_vtk_array_type(
             data_matrix.dtype), 1)
 
     lx, ly, lz = image_data.GetDimensions()

src/openalea/phenomenal/segmentation/maize_stem_detection.py

@@ -109,7 +109,7 @@ def stem_detection(stem_segment_voxel, stem_segment_path, voxels_size,
     window_length = max(4, len(nodes_length) // 8)
     window_length = window_length + 1 if window_length % 2 == 0 else window_length
     smooth_distances = scipy.signal.savgol_filter(
-        numpy.array(distances, dtype=numpy.uint8),
+        numpy.array(distances, dtype=numpy.uint16),
         window_length=window_length,
         polyorder=2)
 

src/openalea/phenomenal/tracking/alignment.py

@@ -181,9 +181,9 @@ def insert_gaps(all_sequences, seq_indexes, alignment):
         for gi in gap_indexes:
 
             if all_sequences2[si].size == 0:
-                all_sequences2[si] = np.full((1, vec_len), np.NAN)
+                all_sequences2[si] = np.full((1, vec_len), np.nan)
             else:
-                all_sequences2[si] = np.insert(all_sequences2[si], gi, np.NAN, 0)
+                all_sequences2[si] = np.insert(all_sequences2[si], gi, np.nan, 0)
 
     return all_sequences2
 

src/openalea/phenomenal/version.py

@@ -3,7 +3,7 @@
 
 major = 1
 minor = 9
-post = 2
+post = 3
 
 __version__ = ".".join([str(s) for s in (major, minor, post)])
 # }}